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Table 3 Comparison of GPMiner with several representative gene promoter annotation programs

From: GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group

Transcriptional regulatory features PromoSer[20] PromH[49] DragonGSF[13] McPromoter[16] GPMiner
Species supported Human, mouse, and rat Human and mouse Mammalian Eukaryote Human, mouse, rat, chimp, and dog
Promoter identification Yes Yes Yes Yes Yes
Map to known gene promoters Yes - - - DBTSS, EPD and Ensembl
Transcription factor binding site - Yes Yes - TRANSFAC public release and JASPAR, MATCH
TATA-box - Yes - Yes Yes
Tandem repeat Yes - - Yes Tandem Repeat Finder
CpG island - - Yes - CpGProD
Over-represented pattern - - - - Yes
DNA stability - - - - Yes
GC content - - Yes - Yes
Co-occurrence of TFBSs - Yes - - Yes
Graphical view Yes - - Yes Yes